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President Barack Obama on Friday accepted the resignation of Veteran Affairs Secretary Eric Shinseki. The move comes two days after an interim VA inspector general investigation found inappropriate scheduling practices, like the ones that were exposed in Phoenix, are “systemic” in the nationwide veterans’ health care system.

VA Secretary Eric Shinseki faced a growing chorus of calls for his resignation following a detailed and scathing report from his own inspector general that found that veterans in Phoenix waited an average of 115 days for an initial doctor visit.

As the White House gave embattled VA Secretary Eric Shinseki more time Thursday, Congress and veterans took direct aim at agency executives who have overseen scheduling abuses spread throughout the nationwide health care system.

The Department of Veterans Affairs inspector general said Wednesday that an ongoing investigation into long wait times, falsified records and veteran deaths has so far confirmed that “inappropriate scheduling practices are systemic throughout” the agency’s health care system.

WASHINGTON — Veterans Affairs Secretary Eric Shinseki said Friday that senior leadership at the Phoenix VA will be fired and executive pay bonuses will be frozen as punishment for systemic scheduling abuses in the nationwide health care system.

In his opening remarks when announcing Shinseki’s resignation later Friday morning, President Barack Obama listed all the changes the secretary had set in motion.

The moves were among a series of initiatives, also including the removal of wait times in employee evaluations and support of legislation that makes it easier to fire executives, unveiled by Shinseki as calls for his resignation spread through Congress over the past two days.

There is widespread frustration on Capitol Hill and among veteran groups that the VA has not done enough after it was revealed the department gamed its health care system by keeping kept off-the-books patient wait lists, which have been blamed for 40 veteran deaths in Phoenix.

Shinseki offered an apology for the deep problems in his department, saying he was misled by staff when he said publicly several months ago that scheduling abuses were isolated to Phoenix.

“I no longer believe it. It is systemic,” said Shinseki, who spoke at a veteran homelessness conference. “I was too trusting of some.”

But the retired four-star general — who received a standing ovation from veteran service groups at the conference — indicated he is not ready to resign his position despite pressure from Congress.

“I also know this leadership and integrity problems can and must be fixed, and now,” he said.

Shinseki said he has started the process of removing senior leadership at the Phoenix facility, which is the epicenter of the widening department scandal, and looking at leadership elsewhere.

Bonuses paid to executives partly based on meeting two-week patient wait times will be suspending through 2014 and the number of days veterans wait for care will no longer be used to evaluate employee performance, he said.

An interim report issued this week by the VA inspector general found that executives manipulated scheduling to meet the department’s wait-list goals, which boosts performance evaluations and led to awards and bonuses.

Besides ousting senior leadership at Phoenix and freezing bonuses, Shinseki said the VA will now support legislation in Congress that would allow the secretary to fire senior executives at will. Currently firings and demotions must be based on formal performance reviews.